Larval size and developmental rate can vary tremendously within and among cohorts because of genetics, environment, and maternal investment. This natural variation in larvae may have effects that span multiple life stages. Here we investigate the effects of larval size and developmental stage on the subsequent life stages of the commercially and ecologically important clam Mercenaria mercenaria. Fifteen days after fertilization, we divided larvae into two groups based on their developmental stage (umbonal or pediveliger) and recorded survival, size, and developmental stage of individuals over the next 4 months. Results revealed that after four months larvae that had only reached the umbonal stage by Day 15 were significantly smaller than those that had reached the pediveliger stage. These smaller and less developed larvae were less successful than the larger and more developed larvae across late larval and juvenile stages. In particular, smaller and less developed larvae were less likely to metamorphose, required more time to metamorphosis, and had lower survival and growth rates. These results suggest that natural variation in larval size and developmental rate can affect recruitment in a variety of ways: (1) Increased time to metamorphosis may increase the cost to larvae via predation or exposure to environmental stress, (2) Decreased proportion of larvae able to metamorphose may directly reduce the number of settlers, and (3) Decreased growth and survival rates for juveniles may reduce the number of new recruits. We also discuss the persistence of natural variation in larval size and developmental rate in light of the observed negative effects associated with smaller and less-developed larvae.